如何在python 3.7中的软件包安装（fcm）期间修复gcc错误
[英]How to fix gcc error during package install (fcm) in python 3.7
问题描述
Recent python user, I am trying to use fcm module to analyze flow cytometry data ( https://pythonhosted.org/fcm/ ). 
最近使用python的用户，我正在尝试使用fcm模块来分析流式细胞仪数据（ https://pythonhosted.org/fcm/ ）。 I find an error related to 'gcc' during pip install. 我在pip安装过程中发现与“ gcc”相关的错误。
Tried updating pip and setuptools, also installed brew and openssl as suggested in How to fix gcc error produced by pip install? 尝试更新pip和setuptools，还按照如何修复pip安装产生的gcc错误中的建议安装了brew和openssl 。 , still finding the same error. ，仍然发现相同的错误。
The terminal output is the following: 终端输出如下：
Collecting fcm
Downloading https://files.pythonhosted.org/packages/b8/50/92e6fcf82b3411def7c5c08a1b9be5fc4d5f4a4ae8eb7c95ee4b0485fbdd/fcm-0.9.1.tar.gz (1.1MB)
100% |████████████████████████████████| 1.1MB 12.9MB/s
Installing collected packages: fcm
Running setup.py install for fcm ... error
Complete output from command /anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/kt/54_zwpj929b852yth43_hj440000gn/T/pip-install-424k_8e4/fcm/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/kt/54_zwpj929b852yth43_hj440000gn/T/pip-record-43efnrvl/install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_py
creating build
creating build/lib.macosx-10.7-x86_64-3.7
creating build/lib.macosx-10.7-x86_64-3.7/fcm
copying src/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/fcm
creating build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/transforms.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/tree.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/annotation.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/fcmdata.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/logicle.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/compensate.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/gate.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/fcmcollection.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/fcmexceptions.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/subsample.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
creating build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
copying src/graphics/plot.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
copying src/graphics/experimental.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
copying src/graphics/plot_gate.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
copying src/graphics/util.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
copying src/graphics/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
copying src/graphics/dimechart.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
creating build/lib.macosx-10.7-x86_64-3.7/fcm/gui
copying src/gui/mpl_qgate.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/gui
copying src/gui/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/gui
copying src/gui/mpl_gate.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/gui
creating build/lib.macosx-10.7-x86_64-3.7/fcm/io
copying src/io/flowjoxml.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/io
copying src/io/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/io
copying src/io/export_to_fcs.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/io
copying src/io/readfcs.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/io
creating build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/mvnpdf.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/partition.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/util.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/modelresult.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/kmeans.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/dime.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/distributions.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/cluster.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/dp_cluster.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/component.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
running build_ext
building 'fcm.core._logicle' extension
creating build/temp.macosx-10.7-x86_64-3.7
creating build/temp.macosx-10.7-x86_64-3.7/src
creating build/temp.macosx-10.7-x86_64-3.7/src/core
creating build/temp.macosx-10.7-x86_64-3.7/src/core/logicle_ext
gcc -Wno-unused-result -Wsign-compare -Wunreachable-code -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -I/anaconda3/include -arch x86_64 -I/anaconda3/include -arch x86_64 -I/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/anaconda3/include/python3.7m -c src/core/logicle_ext/Logicle.cpp -o build/temp.macosx-10.7-x86_64-3.7/src/core/logicle_ext/Logicle.o
warning: include path for stdlibc++ headers not found; pass '-stdlib=libc++' on the command line to use the libc++ standard library instead [-Wstdlibcxx-not-found]
src/core/logicle_ext/Logicle.cpp:3:10: fatal error: 'cstring' file not found
#include <cstring>
^~~~~~~~~
1 warning and 1 error generated.
error: command 'gcc' failed with exit status 1
----------------------------------------
Command "/anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/kt/54_zwpj929b852yth43_hj440000gn/T/pip-install-424k_8e4/fcm/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/kt/54_zwpj929b852yth43_hj440000gn/T/pip-record-43efnrvl/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/kt/54_zwpj929b852yth43_hj440000gn/T/pip-install-424k_8e4/fcm/
I appreciate any further advice 我感谢任何进一步的建议
Edit: After installing Command Line Tools and exporting -stdlib=libc++ 编辑：安装命令行工具并导出-stdlib=libc++
Downloading https://files.pythonhosted.org/packages/b8/50/92e6fcf82b3411def7c5c08a1b9be5fc4d5f4a4ae8eb7c95ee4b0485fbdd/fcm-0.9.1.tar.gz (1.1MB)
100% |████████████████████████████████| 1.1MB 13.3MB/s
Installing collected packages: fcm
Running setup.py install for fcm ... error
Complete output from command /anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/kt/54_zwpj929b852yth43_hj440000gn/T/pip-install-p_ehtvg8/fcm/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/kt/54_zwpj929b852yth43_hj440000gn/T/pip-record-4xk1zm47/install-record.txt --single-version-externally-managed --compile:
running install
running build
running build_py
creating build
creating build/lib.macosx-10.7-x86_64-3.7
creating build/lib.macosx-10.7-x86_64-3.7/fcm
copying src/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/fcm
creating build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/transforms.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/tree.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/annotation.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/fcmdata.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/logicle.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/compensate.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/gate.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/fcmcollection.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/fcmexceptions.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
copying src/core/subsample.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/core
creating build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
copying src/graphics/plot.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
copying src/graphics/experimental.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
copying src/graphics/plot_gate.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
copying src/graphics/util.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
copying src/graphics/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
copying src/graphics/dimechart.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/graphics
creating build/lib.macosx-10.7-x86_64-3.7/fcm/gui
copying src/gui/mpl_qgate.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/gui
copying src/gui/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/gui
copying src/gui/mpl_gate.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/gui
creating build/lib.macosx-10.7-x86_64-3.7/fcm/io
copying src/io/flowjoxml.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/io
copying src/io/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/io
copying src/io/export_to_fcs.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/io
copying src/io/readfcs.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/io
creating build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/mvnpdf.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/partition.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/util.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/__init__.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/modelresult.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/kmeans.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/dime.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/distributions.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/cluster.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/dp_cluster.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
copying src/statistics/component.py -> build/lib.macosx-10.7-x86_64-3.7/fcm/statistics
running build_ext
building 'fcm.core._logicle' extension
creating build/temp.macosx-10.7-x86_64-3.7
creating build/temp.macosx-10.7-x86_64-3.7/src
creating build/temp.macosx-10.7-x86_64-3.7/src/core
creating build/temp.macosx-10.7-x86_64-3.7/src/core/logicle_ext
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/anaconda3/include/python3.7m -c src/core/logicle_ext/Logicle.cpp -o build/temp.macosx-10.7-x86_64-3.7/src/core/logicle_ext/Logicle.o
src/core/logicle_ext/Logicle.cpp:290:4: warning: add explicit braces to avoid dangling else [-Wdangling-else]
else
^
1 warning generated.
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/anaconda3/include/python3.7m -c src/core/logicle_ext/my_logicle.cpp -o build/temp.macosx-10.7-x86_64-3.7/src/core/logicle_ext/my_logicle.o
gcc -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -stdlib=libc++ -I/anaconda3/lib/python3.7/site-packages/numpy/core/include -I/anaconda3/include/python3.7m -c src/core/logicle_ext/my_logicle_wrapper.cpp -o build/temp.macosx-10.7-x86_64-3.7/src/core/logicle_ext/my_logicle_wrapper.o
src/core/logicle_ext/my_logicle_wrapper.cpp:788:3: error: no matching function for call to 'PyBytes_AsStringAndSize'
PyBytes_AsStringAndSize(str, &cstr, &len);
^~~~~~~~~~~~~~~~~~~~~~~
/anaconda3/include/python3.7m/bytesobject.h:103:17: note: candidate function not viable: no known conversion from 'int *' to 'Py_ssize_t *' (aka 'long *') for 3rd argument
PyAPI_FUNC(int) PyBytes_AsStringAndSize(
^
src/core/logicle_ext/my_logicle_wrapper.cpp:2229:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
res = SWIG_AddCast(res);
~~~ ^ ~~~
src/core/logicle_ext/my_logicle_wrapper.cpp:2232:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
res = SWIG_AddCast(res);
~~~ ^ ~~~
src/core/logicle_ext/my_logicle_wrapper.cpp:2454:20: error: use of undeclared identifier 'PyCObject_Import'; did you mean 'PyObject_Init'?
type_pointer = PyCObject_Import((char*)"swig_runtime_data" SWIG_RUNTIME_VERSION,
^~~~~~~~~~~~~~~~
PyObject_Init
/anaconda3/include/python3.7m/objimpl.h:130:24: note: 'PyObject_Init' declared here
PyAPI_FUNC(PyObject *) PyObject_Init(PyObject *, PyTypeObject *);
^
src/core/logicle_ext/my_logicle_wrapper.cpp:2454:37: error: cannot initialize a parameter of type 'PyObject *' (aka '_object *') with an rvalue of type 'char *'
type_pointer = PyCObject_Import((char*)"swig_runtime_data" SWIG_RUNTIME_VERSION,
^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/anaconda3/include/python3.7m/objimpl.h:130:48: note: passing argument to parameter here
PyAPI_FUNC(PyObject *) PyObject_Init(PyObject *, PyTypeObject *);
^
src/core/logicle_ext/my_logicle_wrapper.cpp:2524:23: error: use of undeclared identifier 'PyCObject_FromVoidPtr'
PyObject *pointer = PyCObject_FromVoidPtr((void *) swig_module, SWIG_Python_DestroyModule);
^
src/core/logicle_ext/my_logicle_wrapper.cpp:2547:37: error: use of undeclared identifier 'PyCObject_AsVoidPtr'
descriptor = (swig_type_info *) PyCObject_AsVoidPtr(obj);
^
src/core/logicle_ext/my_logicle_wrapper.cpp:2552:13: error: use of undeclared identifier 'PyCObject_FromVoidPtr'
obj = PyCObject_FromVoidPtr(descriptor, NULL);
^
In file included from src/core/logicle_ext/my_logicle_wrapper.cpp:2800:
In file included from /anaconda3/lib/python3.7/site-packages/numpy/core/include/numpy/arrayobject.h:4:
In file included from /anaconda3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarrayobject.h:12:
In file included from /anaconda3/lib/python3.7/site-packages/numpy/core/include/numpy/ndarraytypes.h:1824:
/anaconda3/lib/python3.7/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-W#warnings]
#warning "Using deprecated NumPy API, disable it with " \
^
src/core/logicle_ext/my_logicle_wrapper.cpp:2919:9: error: use of undeclared identifier 'PyString_Check'; did you mean 'PyMapping_Check'?
if (PyString_Check( py_obj)) return "string" ;
^~~~~~~~~~~~~~
PyMapping_Check
/anaconda3/include/python3.7m/abstract.h:1006:17: note: 'PyMapping_Check' declared here
PyAPI_FUNC(int) PyMapping_Check(PyObject *o);
^
src/core/logicle_ext/my_logicle_wrapper.cpp:2925:9: error: use of undeclared identifier 'PyFile_Check'
if (PyFile_Check( py_obj)) return "file" ;
^
src/core/logicle_ext/my_logicle_wrapper.cpp:2927:9: error: use of undeclared identifier 'PyInstance_Check'; did you mean 'PySequence_Check'?
if (PyInstance_Check(py_obj)) return "instance" ;
^~~~~~~~~~~~~~~~
PySequence_Check
/anaconda3/include/python3.7m/abstract.h:838:17: note: 'PySequence_Check' declared here
PyAPI_FUNC(int) PySequence_Check(PyObject *o);
^
src/core/logicle_ext/my_logicle_wrapper.cpp:3435:14: warning: explicitly assigning value of variable of type 'void *' to itself [-Wself-assign]
clientdata = clientdata;
~~~~~~~~~~ ^ ~~~~~~~~~~
4 warnings and 9 errors generated.
error: command 'gcc' failed with exit status 1
----------------------------------------
Command "/anaconda3/bin/python -u -c "import setuptools, tokenize;__file__='/private/var/folders/kt/54_zwpj929b852yth43_hj440000gn/T/pip-install-p_ehtvg8/fcm/setup.py';f=getattr(tokenize, 'open', open)(__file__);code=f.read().replace('\r\n', '\n');f.close();exec(compile(code, __file__, 'exec'))" install --record /private/var/folders/kt/54_zwpj929b852yth43_hj440000gn/T/pip-record-4xk1zm47/install-record.txt --single-version-externally-managed --compile" failed with error code 1 in /private/var/folders/kt/54_zwpj929b852yth43_hj440000gn/T/pip-install-p_ehtvg8/fcm/
2 个解决方案
解决方案1
0 2019-07-17 13:25:20
如果您要为“ django”安装“ fcm”，则可以通过
pip install django-fcm
解决方案2
0 2019-08-20 22:59:49
I am the maintainer of the FCM codebase, inherited after the original author graduated. 我是FCM代码库的维护者，在原始作者毕业后继承。 FCM was developed to support an hierarchical Dirichlet process (HDP) clustering algorithm. FCM旨在支持分层Dirichlet流程（HDP）聚类算法。 I eventually decided to separate the functionality into 3 different libraries: 我最终决定将功能分成3个不同的库：
- FlowIO : for those that simply need to read FCS data or create new FCS files FlowIO ：对于那些只需要读取FCS数据或创建新的FCS文件的用户
- FlowUtils : for performing basic flow functions (compensation & transforms) FlowUtils ：用于执行基本流量功能（补偿和转换）
- FlowStats : for those looking to use the specific HDP clustering algorithm FlowStats ：适用于希望使用特定HDP聚类算法的用户
All of these have seen significant development since the last version of FCM. 自从上一版FCM以来，所有这些都取得了长足的发展。 In addition to these, we've recently started development on FlowKit , which promises to be a more high-level and (hopefully) more intuitive Python framework for flow cytometry analysis and visualization, including GatingML support. 除此之外，我们最近还开始在FlowKit上进行开发 ，该工具有望成为用于流式细胞术分析和可视化的更高级和（希望）更直观的Python框架，包括GatingML支持。
Note that FlowIO, FlowUtils, and FlowKit are on PyPI and available to install via pip, and are compatible with all platforms including Windows, Mac, and Linux due to the reduced number of dependencies and recent bug fixes. 请注意，FlowIO，FlowUtils和FlowKit在PyPI上，可以通过pip安装，并且由于减少了依赖性和最近的错误修复，因此与所有平台（包括Windows，Mac和Linux）兼容。
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如何为 Python 3.7 安装 PyVimeo？ - How to install PyVimeo for Python 3.7?
Python 如何在运行时修复语法错误 - Python how to fix syntax error during runtime
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